Publication-ready-taxonomic-charts-from-QIIME

Welcome to Xcelris Labs Ltd. GitHub (by Bioinformatics division)

prepare_taxa_charts.py: Ultrafast program to generate publication ready taxonomic pie chart images from QIIME

This script parses the pie_chart.html file (output from plot_taxa_summary.py)
Maps the pie chart and legend image names to corresponding samples.
Copies the files to user defined directory
Rename the files according to sample ids
Merges the pie charts and legends

Usage

python prepare_taxa_charts.py -p pie_charts.html -c /charts_folder -o user_defined_output_folder

List of Python modules used

S. No.	Module
1.	fnmatch
2.	os
3.	getopt
4.	PIL
5.	re
6.	shutil
7.	sys
8.	timeit

Important Note

Prerequisites for prepare_taxa_charts.py:

Python v2.7. The program will not work with Python v3. Python v2.7 was chosen as it is stable.
Legend files should be generated in png format (default is pdf). This could be achieved by running the script plot_taxa_summary.py with the option -t/--type_of_file as png. Given below is an example:

plot_taxa_summary.py -i phylum.txt -l phylum -c pie -o phylum_charts/ -t png

** Note: High resolution images can be generated using the -d, --dpi option for the script plot_taxa_summary.py. See below example (setting the dpi to 100 produce good quality images):

plot_taxa_summary.py -i phylum.txt -l phylum -c pie -o phylum_charts/ -t png -d 100

License

This script is released under GNU GENERAL PUBLIC LICENSE, v3, 29 June 2007

Development and Maintenance

Developed by - Vijay Lakhujani:

Project Scientist, Bioinformatics

NGS division, Xcelris Labs Ltd

vijay.lakhujani@xcelrislabs.com

Let’s connect!

Maintained by @Xcelris-Labs-Ltd on GitHub.

Publication

prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME.

Citing

Please cite: Lakhujani, V. and Badapanda, C., 2017. prepare_taxa_charts. py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME. Genomics Data, 12, pp.97-101.

Official entry for poster presentation

The work was formally presented as scientific poster in Accelerating biology-2018 symposium held during Jan, 9-11, 2018 at C-DAC, Pune, India